Remove image region inside another region

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MARIA RODRIGUEZ SANZ
评论： MARIA RODRIGUEZ SANZ 2018-12-10
Hello!
Does anyone have an idea of how can I remove some regions surrounded by another region? I would like to set the value of these pixels to 0. Both are already segmented and labelled.
This is an example imagesc:
Captura de pantalla 2018-11-27 a las 17.05.14.png
Thank you very much in advanced!
Maria

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回答（3 个）

Image Analyst
Image Analyst 2018-11-27
You could just fill holes in the binarized labeled image, then relabel if you want
binaryImage = imfill(labeledImage > 0, 'holes');
[binaryImage, numberOfBlobs] = bwlabel(binaryImage);
Change connectivity from 4 to 8 or vice versa to see what effect that has.
Attach your labeled image in a .mat file if you need more help.
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MARIA RODRIGUEZ SANZ
MARIA RODRIGUEZ SANZ 2018-12-7
No way! I tried 'holes' and 'noholes' options, but none of them gives the expected output. :(
I can not believe that there is no option for what I'm looking for...it seems so simple...it would give me an excellent ouptput for my study.
Just to remember, I just want to set the child blobs of bwboundaries (blobs inside blobs) to black. Or, what is the same, fill them with zeros!.
Any other ideas? Please...

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MARIA RODRIGUEZ SANZ
Dear Image Analyst,
First of all, thanks a lot for your reply!
In fact, I don't want to fill these holes, but quite the opposite.
In my original grayscale image these subregions correspond -in general- to low intensity regions.
First, I find the edges (The best method I have found to segment adjacent objects in my images. It produces really good results!). Then I delimitate objects by bwboundaries(). (That's because I haven't found any method to fill edges regions...), but it's ok.... The resulting image contains lots of subregions that difficult a lot the subsequent steps (My final purpose is to skeletonize the image and I'm getting messy results because of these undesireable subregions.)
I have to be vey careful playing with thresholds, because I have objects with low intensities that I don't want to loose. That's why it is also complicated to remove those regions with a certain intensity in the original image... (bwpropfilt...).
I know it would not be perfect! but just setting this subregions to 0 would help me a lot!
Captura de pantalla 2018-11-27 a las 18.06.30.png
I attach both my original and labbeled image!
Thank you in advanced again!
Image Analyst
Image Analyst 2018-12-7
编辑：Image Analyst 2018-12-7
I've take your simple blob and made a demo image with some similar ones with different numbers of nested blobs and different levels of nesting. I then made a demo specially for you that removes all inner blobs and leaves only the outermost blob. See attached demo.
clc; % Clear the command window.
close all; % Close all figures (except those of imtool.)
clear; % Erase all existing variables. Or clearvars if you want.
workspace; % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 20;
%===============================================================================
% Read in gray scale demo image.
folder = pwd; % Determine where demo folder is (works with all versions).
baseFileName = 'index.png';
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
% Check if file exists.
if ~exist(fullFileName, 'file')
% The file doesn't exist -- didn't find it there in that folder.
% Check the entire search path (other folders) for the file by stripping off the folder.
fullFileNameOnSearchPath = baseFileName; % No path this time.
if ~exist(fullFileNameOnSearchPath, 'file')
% Still didn't find it. Alert user.
errorMessage = sprintf('Error: %s does not exist in the search path folders.', fullFileName);
uiwait(warndlg(errorMessage));
return;
end
end
rgbImage = imread(fullFileName);
% Display the image.
subplot(2, 3, 1);
imshow(rgbImage, []);
title('Original Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis('on', 'image');
hp = impixelinfo();
% Get the dimensions of the image.
% numberOfColorChannels should be = 1 for a gray scale image, and 3 for an RGB color image.
[rows, columns, numberOfColorChannels] = size(rgbImage)
if numberOfColorChannels > 1
% It's not really gray scale like we expected - it's color.
% Use weighted sum of ALL channels to create a gray scale image.
% grayImage = rgb2gray(rgbImage);
% ALTERNATE METHOD: Convert it to gray scale by taking only the green channel,
% which in a typical snapshot will be the least noisy channel.
grayImage = rgbImage(:, :, 2); % Take green channel.
else
grayImage = rgbImage; % It's already gray scale.
end
% Now it's gray scale with range of 0 to 255.
% Display the histogram of the image.
subplot(2, 3, 2);
[counts, binLocations] = imhist(grayImage);
% Suppress bin 1 because it's so tall
counts(1) = 0;
bar(binLocations, counts);
grid on;
title('Histogram of Image', 'FontSize', fontSize, 'Interpreter', 'None');
%------------------------------------------------------------------------------
% Set up figure properties:
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0, 0.04, 1, 0.96]);
% Get rid of tool bar and pulldown menus that are along top of figure.
% set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Give a name to the title bar.
set(gcf, 'Name', 'Demo by ImageAnalyst', 'NumberTitle', 'Off')
drawnow;
% Binarize the image
% Get the mask where the region is solid.
binaryImage1 = grayImage > 210;
% Display the image.
subplot(2, 3, 3);
imshow(binaryImage1, []);
title('Initial Binary Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis('on', 'image');
hp = impixelinfo();
drawnow;
% Clear borders
binaryImage2 = imclearborder(~binaryImage1);
% Fill holes.
binaryImage2 = imfill(binaryImage2, 'holes');
% Display the image.
subplot(2, 3, 4);
imshow(binaryImage2, []);
title('Filled Binary Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis('on', 'image');
drawnow;
% Get the background color from the upper left pixel
backgroundIntensity = grayImage(1,1);
% Get the final binary image by erasing the first binary image with the latest mask.
finalMask = binaryImage1 & ~binaryImage2;
% Display the image.
subplot(2, 3, 5);
imshow(finalMask, []);
title('Final Binary Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis('on', 'image');
drawnow;
% Use it to mask the original image.
finalImage = grayImage; % Initialize
finalImage(~finalMask) = backgroundIntensity; % Erase outside the mask.
% Display the image.
subplot(2, 3, 6);
imshow(finalImage, []);
title('Final, Masked Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis('on', 'image');
  1 个评论
MARIA RODRIGUEZ SANZ
MARIA RODRIGUEZ SANZ 2018-12-10
Thank you very much Image Analyst!
It helped me a lot! The secret was in imclearborder!. I love this function! hehe!
thanks! thanks! thanks!

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